5 research outputs found
Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam
The first nationwide outbreak of COVID-19 in Vietnam started in late April 2021 and was caused almost exclusively by a single Delta lineage, AY.57. In early 2022, multiple Omicron variants co-circulated with Delta variants and quickly became dominant. The co-circulation of Delta and Omicron happened leading to possibility of co-infection and recombination events which can be revealed by viral genomic data. From January to October 2022, a total of 1028 viral RNA samples out of 4852 positive samples (Ct < 30) were sequenced by the long pooled amplicons method on Illumina platforms. All sequencing data was analysed by the workflow for SARS-CoV-2 on CLC genomics workbench and Illumina Dragen Covid application. Among those sequenced samples, we detected a case of Delta AY.57/Omicron BA.1 co-infection and two cases of infection with Delta AY.57/Omicron BA.2 recombinants which were nearly identical and had different epidemiological characteristics. Since the AY.57 lineage circulated almost exclusively in Vietnam, these results strongly suggest domestic events of co-infection and recombination. These findings highlight the strengths of genomic surveillance in monitoring the circulating variants in the community enabling rapid identification of viral changes that may affect viral properties and evolutionary events
Spatiotemporal evolution of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021
We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions
COVID-19 patients hospitalized after the fourth wave of the pandemic period in Vietnam: Clinical, laboratory, therapeutic features, and clinical outcomes
Background/Purpose: Despite having relatively high COVID-19 vaccine coverage in Vietnam, a fraction of COVID-19 patients required hospitalization due to severe symptoms. The purpose of this study was to describe the clinical, laboratory, complications, and treatment of COVID-19 patients hospitalized during the pandemic's fourth wave. Methods: Genome sequencing was performed on COVID-19 patients. Data on clinical characteristics, treatment, complications, and outcomes were consistently collected. Results: The clinical classifications were mild (37.43%), moderate (24.2%), and severe (38.37%). Patients with co-morbidities, high fever >39 °C, hypertension, tachycardia, tachypnea, and SpO2<90%, had a 1.2–4 folds higher of severe progression than those with mild/moderate. Serious consequences were much more common in the severe patients than in the mild/moderate. The respiratory system of severe patients was generally documented as fine, coarse crackles, and CT scanner shown ground glass, consolidation, and opacity, with Delta variant accounting for 92.6%. Complications were common in the severe patients, including bacteria pneumonia (36.42%), ARDS (61.11%), blood clotting disorder (7.14%), infection (46.92%), and acute kidney injury (12.35%). Antiviral, antifungal, corticosteroid, anticoagulant, and ECMO regimens were utilized. Patients died mostly as a result of co-morbidities, low SpO2, lung injury, and complications such as bacterial + fungal pneumonia (83.9%), ARDS (83.9%), bacteremia (56.5%), injury acute renal failure (27.4%), and coagulopathy (12.9%). Conclusion: Severe and critical COVID-19 patients frequently have several comorbidities, multiple lung lesions along with a variety of clinical signs. Despite receiving antivirals, antibiotics, corticosteroids, anticoagulants, and even ECMO therapy, the patient encountered multiple complications, with a fatality rate of up to 38.27%
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Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates.
Screening the genetic diversity of 45 Yarrowia lipolytica strains identified five candidates with unique metabolic capability and robustness in undetoxified switchgrass hydrolysates, including superior lipid production and efficient pentose sugar utilization. Here, we report the genome sequences of these strains to study their robustness and potential to produce fuels and chemicals